DAMEfinder: DAMEfinder: Method to detect allele-specific methylation...

DAMEfinderR Documentation

DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R.

Description

The package allows the user to extract an ASM score in two ways: either from a bismark bam file(s) and VCF file(s), or from the output from methtuple. Either way the final output is a list of regions with diferential allele-specific methylated between groups of samples of interest. The package also provides functions to visualize ASM at the read level or the score level

DAMEfinder functions

calc_asm extracts ASM for pairs of CpG sites from a methtuple file, calc_derivedasm extracts ASM at each CpG site linked to a SNP from the VCF file. Both functions generate a RangedSummarizedExperiment, which is the input for the main function find_dames, that generates a data.frame with regions exhibiting differential ASM between a number of samples.

Author(s)

Stephany Orjuela sorjuelal@gmail.com

Dania Machlab

Mark D Robinson mark.robinson@imls.uzh.ch


markrobinsonuzh/DAMEfinder documentation built on April 7, 2023, 6:37 a.m.